def bel_process_belrdf():
"""Process BEL RDF and return INDRA Statements."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
belrdf = body.get('belrdf')
bp = bel.process_belrdf(belrdf)
return _stmts_from_proc(bp)
def bel_process_belrdf():
"""Process BEL RDF and return INDRA Statements."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
belrdf = body.get('belrdf')
bp = bel.process_belrdf(belrdf)
return _stmts_from_proc(bp)
def test_get_transcription():
print("Opening file")
with open(test_rdf_myc, 'rt') as fh:
rdf_str_myc = fh.read()
print("Process BEL RDF")
bp = bel.process_belrdf(rdf_str_myc)
transcription_stmts = []
for stmt in bp.statements + bp.indirect_stmts:
if isinstance(stmt, RegulateAmount):
transcription_stmts.append(stmt)
assert len(transcription_stmts) == 8
pass
def test_get_transcription():
print("Opening file")
with open(test_rdf_myc, 'rt') as fh:
rdf_str_myc = fh.read()
print("Process BEL RDF")
bp = bel.process_belrdf(rdf_str_myc)
transcription_stmts = []
for stmt in bp.statements + bp.indirect_stmts:
if isinstance(stmt, RegulateAmount):
transcription_stmts.append(stmt)
assert len(transcription_stmts) == 8
pass
def bel_process_belrdf():
"""Process BEL RDF and return INDRA Statements."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
belrdf = body.get('belrdf')
bp = bel.process_belrdf(belrdf)
if bp and bp.statements:
stmts = stmts_to_json(bp.statements)
res = {'statements': stmts}
return res
else:
res = {'statements': []}
return res
def post(self):
"""Process BEL RDF and return INDRA Statements.
Parameters
----------
belrdf : str
A BEL/RDF string to be processed. This will usually come from
reading a .rdf file.
Returns
-------
statements : list[indra.statements.Statement.to_json()]
A list of extracted INDRA Statements.
"""
args = request.json
belrdf = args.get('belrdf')
bp = bel.process_belrdf(belrdf)
return _stmts_from_proc(bp)
def test_process_belrdf():
with open(test_rdf_nfkb, 'rb') as fh:
rdf_str_nfkb = fh.read().decode('utf-8')
bp = bel.process_belrdf(rdf_str_nfkb)
assert_pmids(bp.statements)
unicode_strs(bp.statements)
def test_process_belrdf():
with open(test_rdf_nfkb, 'rb') as fh:
rdf_str_nfkb = fh.read().decode('utf-8')
bp = bel.process_belrdf(rdf_str_nfkb)
assert_pmids(bp.statements)
unicode_strs(bp.statements)
sdict[s]=None
return mon(sdict)
def add_initial(model, pattern, value):
"""Add initial condition; if an initial condition for this pattern
already exists, override it."""
complex_pattern = pysb.as_complex_pattern(pattern)
for other_cp, other_value in model.initial_conditions:
if complex_pattern.is_equivalent_to(other_cp):
model.initial_conditions.remove((other_cp, other_value))
model.initial(complex_pattern, value)
# Generate model rules via indra
pa = PysbAssembler()
bp = bel.process_belrdf('RAS_combined.rdf')
pa.add_statements(bp.statements)
model = pa.make_model(initial_conditions=False)
# Useful shortcuts to access model components
m = model.monomers
p = model.parameters
# Add ligand to the model
model.add_component(Monomer('EGF'))
model.add_component(Parameter('kf_ee_act', 1e-6))
model.add_component(
Rule('EGF_activates_EGFR',
m['EGF']() + m['EGFR']({'Kinase':'inactive'}) >>
m['EGF']() + m['EGFR']({'Kinase':'active'}),
p['kf_ee_act']))